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The Pathway Tools software.

Peter D Karp1, Suzanne Paley, Pedro Romero

  • 1Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA. pkarp@ai.sri.com

Bioinformatics (Oxford, England)
|August 10, 2002
PubMed
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Pathway Tools is a reusable software environment for building Pathway/Genome Databases (PGDBs). These databases integrate organismal data, aiding bioinformatics research and model-organism database creation.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Bioinformatics research necessitates adaptable software solutions for constructing model-organism databases (MODs).
  • Existing tools may lack the reusability and production quality required for comprehensive biological data integration.

Purpose of the Study:

  • To introduce Pathway Tools, a robust software environment for creating Pathway/Genome Databases (PGDBs).
  • To detail the components and functionalities of Pathway Tools for PGDB development and management.

Main Methods:

  • Development of the PathoLogic component for PGDB creation from annotated genomes.
  • Implementation of the Pathway/Genome Navigator for data querying, visualization, and web publishing.
  • Integration of Pathway/Genome Editors for interactive PGDB updates and the Pathway Tools ontology for schema definition.

Related Experiment Videos

  • Utilization of the Ocelot object database system for efficient data management.

    • Main Results:

    • Pathway Tools provides a production-quality environment for building PGDBs, exemplified by EcoCyc.
    • The system integrates diverse biological data, including genes, proteins, and metabolic/genetic networks.
    • The software has been successfully employed to construct PGDBs for 13 organisms by internal and external users.

    Conclusions:

    • Pathway Tools offers a comprehensive and reusable solution for creating and managing Pathway/Genome Databases.
    • The software facilitates the integration of complex biological data, advancing model-organism database development.
    • Its successful application across multiple organisms demonstrates its utility and scalability in bioinformatics.